Gomes was in because Farrell liked him over Nava for whatever reason. I will refuse the appeal to authority ("Well we don't have the info the manager does" and the like) and say it was somewhat suboptimal, but not by a margin that killed anybody.
Ellsbury I think we are just talking about some very large dollar figures - and if ownership is concerned about the luxury tax, which is their prerogative, that is a legitimate concern. The Red Sox are doing some due diligence, and they do have a little bit of leverage here. They have a substitute with potential, a fan base that will not punish them for the short term - winning a title will sell enough pink hats to assure that at last early - and a team without essentially no real holes. Yes, catcher is a problem since you'd get a lot of passed balls without one - but replacement level is so low that being below average there doesn't really hurt you that badly.
The number of teams that need a guy like him AND can pay the price is not high - just matching teams with need, I'd put the Rangers at the top of the list, but yes the Yankees are always a factor. That said, some more imaginative options to me might be San Francisco or Anaheim (who is in that arms race with the Dodgers for SoCal moolah). Frankly if I were Pittsburgh, the marginal revenue calculations could favor a high dollar, short offer, although I'd be surprised if that ever happened. (they were a playoff team who got zero from their RF spot for most of the season, the marginal boost Ellsbury could give might actually create a business case).